dipy_track_pft#

Synopsis#

Workflow for Particle Filtering Tracking.

This workflow uses a saved peaks and metrics (PAM) file as input. See [1] for further details about the method.

Usage#

dipy_track_pft [OPTIONS] pam_files wm_files gm_files csf_files seeding_files

Input Parameters#

  • pam_files

    Path to the peaks and metrics files. This path may contain

    wildcards to use multiple masks at once.

  • wm_files

    Path to white matter partial volume estimate for tracking (CMC).

  • gm_files

    Path to grey matter partial volume estimate for tracking (CMC).

  • csf_files

    Path to cerebrospinal fluid partial volume estimate for tracking (CMC).

  • seeding_files

    A binary image showing where we need to seed for tracking.

General Options#

  • --step_size

    Step size (in mm) used for tracking.

  • --seed_density

    Number of seeds per dimension inside voxel.

    For example, seed_density of 2 means 8 regularly distributed points in the voxel. And seed density of 1 means 1 point at the center of the voxel.

  • --pmf_threshold

    Threshold for ODF functions.

  • --max_angle

    Maximum angle between streamline segments (range [0, 90]).

  • --pft_back

    Distance in mm to back track before starting the particle filtering tractography. The total particle filtering tractography distance is equal to back_tracking_dist + front_tracking_dist.

  • --pft_front

    Distance in mm to run the particle filtering tractography after the the back track distance. The total particle filtering tractography distance is equal to back_tracking_dist + front_tracking_dist.

  • --pft_count

    Number of particles to use in the particle filter.

  • --save_seeds

    If true, save the seeds associated to their streamline in the ‘data_per_streamline’ Tractogram dictionary using ‘seeds’ as the key.

  • --min_wm_pve_before_stopping

    Minimum white matter pve (1 - stopping_criterion.include_map - stopping_criterion.exclude_map) to reach before allowing the tractography to stop.

Output Options#

  • --out_dir

    Output directory. (default current directory)

  • --out_tractogram

    Name of the tractogram file to be saved.

References#

Garyfallidis, E., M. Brett, B. Amirbekian, A. Rokem, S. Van Der Walt, M. Descoteaux, and I. Nimmo-Smith. Dipy, a library for the analysis of diffusion MRI data. Frontiers in Neuroinformatics, 1-18, 2014.